I have been shooting a series of microprocessor chip sets with Helicon Remote and processing them in Helicon Focus and they have been working perfectly. After 30 image stcks processed without errors and with no changes in settings, equipment or anything else, I am now getting an internal render error 5 on a new stack. When I open the images in the stack, I see that every other image is rotated. My camera is a Canon 5D Mark III with MP-E 65mm with Stack Shot 3x. I have verified that auto rotate is off. I have also tired it with autorotate on, and am getting the same error.How can I resolve this issue?

The problem is probably with the image orientation EXIF tag. You can fix it with some image editing software. The root cause must be the camera body - disable the orientation sensor in the body settings.

Are you working on a copy stand? I had a similar problem because, when it is pointing straight down, the camera cannot decide if it is in portrait or landscape mode. I solved it by tilting the entire stand a few degrees.